The working groups and committees of the abovementioned EU institutions and bodies discuss and decide matters of relevance to eu-LISA and thus have a directly influence on the Agency's activities. The Agency actively participates in the relevant working groups and committees of the EU Council, the European Commission and the European Parliament. eu-LISA is most involved in groups working on matters directly related to SIS II, VIS and Eurodac but also follows the work of groups dealing with Schengen, police cooperation and information exchange.

​Cooperation with the European Data Protection Supervisor is of particular significance due to the nature of the tasks of the Agency to manage three of the largest EU information systems in the area of feedom, security and justice. Equally, close working relations with the European Court of Auditors are paramount to ensure compliance with the EU rules and regulations in auditing to ensure public accountability and sound financial management.​